Sim chromatogram and odd baseline shifts

[LabProARW]

My TIC of datasim.ms chromatogram plot has a sharp baseline drop after one of my peaks. After another peak in the same run the baseline shifts up quite a bit. There are more shifts relational to other peaks as well, certainly it has to affect the integration and abundance determinations. Would some kind soul direct me to how in MassHunter acquisition and Enhanced Chemstation Data Analysis to know what is causing this? I would post a jpg image but I don't have an address to upload the image to.

I believe I just don't understand datasim.ms baseline because I think of it like a normal GC signal plot and integration.

Thank you in advance.

[wss]

My TIC of datasim.ms chromatogram plot has a sharp baseline drop after one of my peaks. After another peak in the same run the baseline shifts up quite a bit. There are more shifts relational to other peaks as well, certainly it has to affect the integration and abundance determinations. Would some kind soul direct me to how in MassHunter acquisition and Enhanced Chemstation Data Analysis to know what is causing this? I would post a jpg image but I don't have an address to upload the image to.

I believe I just don't understand datasim.ms baseline because I think of it like a normal GC signal plot and integration.

Thank you in advance.

That's normal, the SIM mode baseline will abruptly shift up and down depending on the associated baseline noise for the masses in the different SIM groups programmed in as part of the acquisition parameters. Baseline noise in the mass spec is not uniform across the whole mass range, so when it starts monitoring a different group of ions in SIM mode, the associated baseline noise will suddenly change too.

The shifts shouldn't affect your quantitation, because the peak will be integrated relative to the baseline at that specific retention time. Your standards will experience the same shift, so this will be accounted for in the calibration.

[LabProARW]

Thank you wss from Australia for being kind enough to help a GCMS noob!

[wss]

Thank you wss from Australia for being kind enough to help a GCMS noob!

No worries!